How to search plasmid sequence for restriction sites and resistance genes? - (Mar/03/2008 )
I acquired a plasmid recently, and I have the complete DNA sequence. However, the plasmid map they gave me is lacking in details (see jpeg). I can't tell from the map what the restriction sites are, nor the type of bacterial resistance. Moreover, I don't know where the gene of interest is inserted in the vector. It's a pUC19 vector. My question is are there software programs out there that I can use to find these features automatically within the plasmid sequence? Are there free programs? Before you ask, I have requested a more detailed cDNA map, but they haven't got back to me yet. I have attached the map. The inserted gene begins with "R" (but I have deleted the rest of the name).
try to download vector NTI (its free) from invitrogen's site. They have sequences for some commonly used plasmids and all of their plasmids. there have the the sequence for pUC19.
I'm using a Mac with 10.5 (Leopard), and according to the website the software only runs on 10.3 (not 10.4, and I'm assuming not 10.5, although it doesn't say). I guess I can try it, and see what happens.
I found a program called EnzymeX from the same folks who created Papers for OS X. It appears that EnzymeX will be useful for finding restriction sites.
also google 'restrict' and the first result is a good source. its an online program